Endothelial cell differentiation CMO library processing

This repository contains the commands used to reconstruct per-channel GEX and CMO FASTQs from the mixed 10x multiome / CMO 5 timepoints sequencing data.

Summary of the steps:

1. Concatenate the FASTQs
2. Separate CMO from GEX with splitcode
3. Trim CMO R1 file
4. Quantify CMO tags per barcode using the kite workflow from kb

10X Genomics multi-ome 5 timepoints:

README.md

10X Genomics multi-ome 15 timepoints:

README.md